Hi Lewis, This is a great chance to demonstrate some of the things that can be done with the new fingerprint generation code. It's going to take me a bit to put this together (it's all new enough that I'm still not quite "fluent"), but I will try to get an example put together over the next couple of days.
-greg On Wed, Jan 30, 2019 at 4:59 AM Lewis Martin <lewis.marti...@gmail.com> wrote: > Hi rdkitters, > I'd like to compare the similarity of torsion/atom pair FPs using standard > atomic numbering with those using pharmacophore types, like the 'CATS' atom > typing developed by Gisbert Schneider, and hoped someone has some advice > here. *CATS* is a pharmacophore atom typing system with these types: > H-bond donor, H-bond acceptor, positive, negative, lipophilic, and CATS2 > has 'aromatic'. These are described in: *“Scaffold‐Hopping” by > Topological Pharmacophore Search: A Contribution to Virtual Screening. *It > seems pretty close to the Gobbi 2D pharmacophore typing, or the features > used in FCFP. > > Ive no problem detecting the atom types - I borrowed code from the open > source PyBioMed - but I'm stuck at the next step. How to change the atoms > into their pharmacophore types to then make a torsion or atom pair > fingerprint using RDKit? What I've tried so far is to just set the atomic > number to some series of 5 atoms not normally seen in drug like molecules, > like 40-44. This is silly but it seems to work. The only issue is trouble > kekulizing the molecules for display. Is there a better way? > > > Here's a snippet to demonstrate what I mean, it's adapted from PyBioMed > and any errors are probably mine: > https://github.com/ljmartin/snippets/blob/master/atom_typing_snippet.ipynb > > Thanks for your time! > lewis > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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